[Bioc-devel] biomaRt uswest mirror ERROR

[Shepherd, Lori]

Ok. Thanks Mike.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Mike Smith <grimbough at gmail.com>
Sent: Tuesday, April 24, 2018 12:17:58 PM
To: Shepherd, Lori
Cc: bioc-devel at r-project.org
Subject: Re: biomaRt uswest mirror ERROR

Hi Lori,

There should be no issue with switching to an alternative mirror with regards to the content.

However, in the current release you will also need to set the argument ensemblRedirect = FALSE otherwise it'll end up at the uswest mirror regardless of the host you specify.  This is not the case in the devel version, as I've disabled the geo-redirect by default after talking to the people at Ensembl, and the host argument is always obeyed.

Cheers,

Mike

On 24 April 2018 at 17:30, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote:

Hello,


OrganismDbi is failing.

http://bioconductor.org/checkResults/3.7/bioc-LATEST/OrganismDbi/malbec2-checksrc.html


It appears that this link is not available for the uswest mirror:

http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt


when specifying the host = "uswest.ensembl.org<http://uswest.ensembl.org>"


Is there any consequence to changing this to the us east mirror instead of west as that one appears to be up?

It has been a week since this weblink has been unavailable and wasn't sure what the time frame of having it back up was.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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